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Results: 14


MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis.

LaMarche BL, Crowell KL, Jaitly N, Petyuk VA, Shah AR, Polpitiya AD, Sandoval JD, Kiebel GR, Monroe ME, Callister SJ, Metz TO, Anderson GA, Smith RD.

BMC Bioinformatics. 2013 Feb 12;14:49. doi: 10.1186/1471-2105-14-49.


DanteR: an extensible R-based tool for quantitative analysis of -omics data.

Taverner T, Karpievitch YV, Polpitiya AD, Brown JN, Dabney AR, Anderson GA, Smith RD.

Bioinformatics. 2012 Sep 15;28(18):2404-6. doi: 10.1093/bioinformatics/bts449. Epub 2012 Jul 19.


Diurnal rhythms result in significant changes in the cellular protein complement in the cyanobacterium Cyanothece 51142.

Stöckel J, Jacobs JM, Elvitigala TR, Liberton M, Welsh EA, Polpitiya AD, Gritsenko MA, Nicora CD, Koppenaal DW, Smith RD, Pakrasi HB.

PLoS One. 2011 Feb 22;6(2):e16680. doi: 10.1371/journal.pone.0016680.


Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.

Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, Polpitiya AD, Adkins JN, Schramm G, Purvine SO, Lopez-Ferrer D, Weitz KK, Eils R, König R, Smith RD, Palsson BØ.

Mol Syst Biol. 2010 Jul;6:390. doi: 10.1038/msb.2010.47.


Liquid Chromatography Mass Spectrometry-Based Proteomics: Biological and Technological Aspects.

Karpievitch YV, Polpitiya AD, Anderson GA, Smith RD, Dabney AR.

Ann Appl Stat. 2010;4(4):1797-1823.


Novel Ser/Thr protein phosphatase 5 (PP5) regulated targets during DNA damage identified by proteomics analysis.

Ham BM, Jayachandran H, Yang F, Jaitly N, Polpitiya AD, Monroe ME, Wang L, Zhao R, Purvine SO, Livesay EA, Camp DG 2nd, Rossie S, Smith RD.

J Proteome Res. 2010 Feb 5;9(2):945-53. doi: 10.1021/pr9008207.


DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets.

Petyuk VA, Mayampurath AM, Monroe ME, Polpitiya AD, Purvine SO, Anderson GA, Camp DG 2nd, Smith RD.

Mol Cell Proteomics. 2010 Mar;9(3):486-96. doi: 10.1074/mcp.M900217-MCP200. Epub 2009 Dec 17.


Combined pulsed-Q dissociation and electron transfer dissociation for identification and quantification of iTRAQ-labeled phosphopeptides.

Yang F, Wu S, Stenoien DL, Zhao R, Monroe ME, Gritsenko MA, Purvine SO, Polpitiya AD, Tolić N, Zhang Q, Norbeck AD, Orton DJ, Moore RJ, Tang K, Anderson GA, Pasa-Tolić L, Camp DG 2nd, Smith RD.

Anal Chem. 2009 May 15;81(10):4137-43. doi: 10.1021/ac802605m.


Using systems biology to simplify complex disease: immune cartography.

Polpitiya AD, McDunn JE, Burykin A, Ghosh BK, Cobb JP.

Crit Care Med. 2009 Jan;37(1 Suppl):S16-21. doi: 10.1097/CCM.0b013e3181920cb0.


Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled "universal" reference sample.

Qian WJ, Liu T, Petyuk VA, Gritsenko MA, Petritis BO, Polpitiya AD, Kaushal A, Xiao W, Finnerty CC, Jeschke MG, Jaitly N, Monroe ME, Moore RJ, Moldawer LL, Davis RW, Tompkins RG, Herndon DN, Camp DG, Smith RD; Inflammation and the Host Response to Injury Large Scale Collaborative Research Program.

J Proteome Res. 2009 Jan;8(1):290-9. doi: 10.1021/pr800467r.


DAnTE: a statistical tool for quantitative analysis of -omics data.

Polpitiya AD, Qian WJ, Jaitly N, Petyuk VA, Adkins JN, Camp DG 2nd, Anderson GA, Smith RD.

Bioinformatics. 2008 Jul 1;24(13):1556-8. doi: 10.1093/bioinformatics/btn217. Epub 2008 May 3.


Plasticity of the systemic inflammatory response to acute infection during critical illness: development of the riboleukogram.

McDunn JE, Husain KD, Polpitiya AD, Burykin A, Ruan J, Li Q, Schierding W, Lin N, Dixon D, Zhang W, Coopersmith CM, Dunne WM, Colonna M, Ghosh BK, Cobb JP.

PLoS One. 2008 Feb 13;3(2):e1564. doi: 10.1371/journal.pone.0001564.


Application of proteomics in the discovery of candidate protein biomarkers in a diabetes autoantibody standardization program sample subset.

Metz TO, Qian WJ, Jacobs JM, Gritsenko MA, Moore RJ, Polpitiya AD, Monroe ME, Camp DG 2nd, Mueller PW, Smith RD.

J Proteome Res. 2008 Feb;7(2):698-707. Epub 2007 Dec 20.


Splenic CD4+ T cells have a distinct transcriptional response six hours after the onset of sepsis.

McDunn JE, Turnbull IR, Polpitiya AD, Tong A, MacMillan SK, Osborne DF, Hotchkiss RS, Colonna M, Cobb JP.

J Am Coll Surg. 2006 Sep;203(3):365-75.

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